Gene with interruptions

Alternative splicing

Mikhail Gelfand, Post-science

There is a central dogma of molecular biology formulated by Francis Crick: DNA makes RNA, RNA makes protein. There is a basic process, namely transcription, which is copying information from DNA into RNA. And there is translation – this is the reading of RNA and, accordingly, protein synthesis based on the instructions that are in the RNA. This is enough for a school textbook.

For a university textbook, it is already necessary to understand that there is a lot going on between transcription and translation. Or rather, like this: nothing happens in bacteria, but you and I, that is, organisms that have a nucleus, are changing. When a transcript is read in the nucleus, it changes a lot before it gets into the cytoplasm and starts working as a matrix RNA to synthesize a protein. This is called "processing".

A DNA fragment is a gene that continuously encodes a protein. This is what people who work with bacteria are used to. After all, initially molecular biology was based on the study of bacteria – simply because it is easier to grow them. It turned out that our genes are not arranged that way. We have them divided into separate coding regions, which are called "exons". And between them there are inserts that do not encode anything. For this discovery, the 1993 Nobel Prize was awarded to British biochemist Richard Roberts and American geneticist Phillip Sharp. They saw this phenomenon experimentally in an electron microscope. DNA and RNA were hybridized, and large DNA loops appeared that do not hybridize with RNA. During hybridization, the corresponding sites simply mate into the same double helix as Watson-Krikovskaya, only not DNA-DNA, but DNA-RNA. Normally there is one strand of DNA and another strand of DNA. And then you can take one strand of DNA and the other strand of RNA and hybridize in the same way. Where RNA is read with DNA, it hybridizes because it is complementary. The transcription process is arranged on the same complementary pairs. Where there was something superfluous in the DNA that did not get into the RNA, a loop is formed. This is what scientists saw in the microscope and realized that there are extra inserts in the DNA.

For people with a philological education, it is necessary to imagine a magazine with advertising inserts or a TV show in which there is a main text, and advertising inside it. My sister had a wonderful tape recorder at the time, which recorded programs that she was interested in, and at the same time removed the commercial breaks. This is pure splicing. A separate good question is where it came from, why is it even necessary? Evolutionarily, this seems to have arisen at the moment when the first eukaryotes, cells with a nucleus, appeared. Introns, apparently, were parasites, and splicing was a way to clean genes from them. We see that in fact most genes do have introns. It turns out that you have a splicing process, that is, the process of cutting out meaningless inserts at the transcript level. Rather, the transcript is read as it is, and matures in the nucleus, introns are cut out, and exons are stitched together.

You can leave some exon in part of the transcripts, and cut out some of the transcripts. As a result, different proteins will be read from one gene: one will have an additional insert, and the other will not have it. Or, for example, you can make two different exons, so that one of these exons is inserted into a part of the matrix RNAs, and another one is inserted into a part. And again you will have proteins that are identical everywhere, but differ in some one area. Alternative splicing is a situation where you have proteins that are partially identical and partially completely different.

It turned out that a lot of genes are alternatively spliced. For quite a long time it was believed that this was some kind of exotic. In Sharp's Nobel Lecture, it was estimated that about 5% of human genes are alternatively spliced. When we began to study matrix RNAs en masse, when methods appeared that allow us to determine the RNA sequences of a very large number of genes at once, it turned out that about a third of the genes are alternatively spliced. Then it turned out that even more. That is, it is not exotic, but a mass process. Apparently, this is an evolutionarily convenient thing. School understanding of alternative splicing suggests that it is a mechanism that allows you to increase the diversity of proteins without increasing the number of genes. To some extent, this is nonsense, because if you need a variety of proteins, then you can breed as many genes as you want. Only 2% of our genome encodes proteins, everything else is introns, intergenic sites, repeats. If you need twice as many proteins, then make twice as many genes. The genome will not increase from this. Apparently, in fact, the evolutionary reason that alternative splicing exists is in another.

One thing is approximately clear when you need proteins that are absolutely identical in some parts, and in other parts, on the contrary, different. The simplest example is receptors and antibodies. You have a cell of the immune system that can recognize a foreign antigen and start producing antibodies against that antigen. She has a receptor that recognizes, and there is a secreted immunoglobulin, an antibody that recognizes the same thing. The cell begins to produce an antibody only after recognizing this antigen. But now it is clear that the receptor and the immunoglobulin itself must have the same specificity. It's a bit silly to find out some antigen and start making an antibody against another antigen. At the same time, the proteins are different: one is a membrane receptor, it is anchored in the membrane, and only the recognizing part is released from it, and the other is secreted. There is a healthy protein that, on the contrary, comes out of the cell, learns. And it has many more parts that ensure the destruction of the antigen and then interact with the rest of the immune system. You do all this by alternative splicing.

There is a common part that is present in all read matrices and performs recognition. Different parts resulting from alternative splicing are responsible for different functions. You can't do it with two genes. In this case, you are the supreme genetic engineer. As soon as you have done this with two different genes, independent mutations begin to accumulate in the recognizing parts of one and the other, and even if they were identical at first, a random mutation process will pull them apart.

Apparently, the evolutionary benefit of alternative splicing is precisely that quite often we do not need similar proteins, but proteins that are similar in a very special sense: somewhere they are identical, and somewhere they are not at all similar. On the other hand, in a general sense, alternative splicing is useful because it makes evolution more agile. We have observed that alternatively spliced exons are quite often young exons that have emerged recently. A person has it, but a mouse does not. The gene is the same, the human has an additional exon that the mouse does not have, and most likely it will be an alternatively spliced exon. In molecular evolution, this situation seems to occur quite often.

Splicing is often wrong. That is, the excision of exons is not absolutely one hundred percent correct. You get matrices with errors: something is cut out of them, something is inserted into them wrong. There is a special mechanism for suppressing and destroying these erroneous matrix RNAs. Again, philologists will be pleased that there is a special mechanism for destroying nonsense. That's what nonsense is called-mediated decay.

On the other hand, it's a wonderful opportunity to experiment with new features. If the matrix, mistakenly spliced, is not destroyed for some reason, then you will get a protein that is in most parts the same as it was before, correctly read, and some part is slightly different. It may well modify the function. How does evolution work? These are random changes and the selection that affects them. And here we have a wonderful mechanism for generating the initial diversity, most of which is nonsense, but something may be minimally useful. If a useful product is obtained due to a splicing error, then positive selection mechanisms are activated further. This is Darwinian classical evolution described a million times. Darwin wrote about this, he just didn't know such words. Gradually, you have a protein with a new function. And this, among other things, turned out to be a wonderful mechanism for increasing diversity. But not in the sense that we increase diversity in one organism, but the generation of diversity in the evolutionary sense. This is the second evolutionary meaning of alternative splicing.

About the author:
Mikhail Gelfand – Doctor of Biological Sciences, Professor, Skoltech Life Sciences Center, Deputy Director of the Institute of Information Transmission Problems of the Russian Academy of Sciences, member of the European Academy, winner of the A.A. Prize. Baeva, member of the Public Council of the Ministry of Education and Science.

Portal "Eternal youth" http://vechnayamolodost.ru